Biology subjects

Koren, K.

Publications and source records attributed to Koren, K..

8 recordsLinked to original sources

bioRxiv2026

Pericentromeric repeat copy number tunes heterochromatin dosage to control chromosome segregation and gene expression in fission yeast

Centromeres are essential for chromosome segregation, yet in many genomes they are composed entirely of rapidly evolving repetitive DNA, embedded in other repetitive DNA that forms pericentromeric heterochromatin. Due to the difficulties of manipulating these repeat-rich regions, how the relative size of pericentromeric repeat regions influences chromosome segregation remains an open question. Here, we take advantage of the tractable Schizosaccharomyces pombe system by combining population-level analysis, complete long-read assemblies, and engineered near-isogenic strains to test how pericentromeric repeat copy number affects chromosome biology in its native context. We find that pericentromeric dh/dg arrays on chromosome 3 vary almost tenfold in size among natural S. pombe isolates, ranging from 35 to 265 kb. We converted this natural diversity into an experimental system of nearly isogenic strains that primarily differ in pericentromere size (35 to >350 kb). We found that pericentromere size does not alter baseline growth under standard conditions. However, larger pericentromeres alter transcriptional output and sensitize cells to spindle stress. We show that this spindle-stress phenotype depends on heterochromatin: loss of the H3K9 methyltransferase Clr4 abolishes size-dependent differences, whereas artificial targeting of the Chromosomal Passenger Complex to heterochromatin partially rescues the defect. Thus, we find that larger pericentromeres act as sinks for limiting regulatory factors, weakening their effective concentration at centromeres and compromising faithful chromosome segregation under stress. These results establish that naturally occurring copy-number variation within repetitive pericentromeric DNA is not merely noise, but a functional source of variation in chromosome segregation and gene regulation. Our work provides an experimentally tractable framework for understanding how repeat expansion in centromere-proximal heterochromatin influences chromosome behavior across eukaryotes.

genetics↗

bioRxiv2025

Let-them-stick: Increasing biofilm formation by the acetogen Sporomusa ovata through adaptive laboratory evolution

Acetogenic bacteria are attractive biocatalysts for the conversion of CO2 with H2 into acetate, as in gas fermentation. Gas fermentation reactors may benefit from biofilm formation, but cell attachment by acetogens is often limited. This study indeed found that the acetogen Sporomusa ovata 2663 was mainly planktonic and aimed to increase its biofilm formation through adaptive laboratory evolution. The adaptation strategy consisted of growing S. ovata on plastic carriers in bottles with a H2:CO2 headspace and transferring few carriers to bottles with fresh carriers over eight serial transfers. This procedure resulted in the evolved S. ovata 2663-BF, which had a consistent increased propensity to attach. In heterotrophic growth conditions, four times more cells attached to the bottom of well plates in comparison to the wild type. Moreover, twice as many cells adhered to carriers when grown on H2:CO2. This improved attachment, however, did not lead to higher acetate production rates in simple trickle bed reactors, as the used experimental setup likely stimulated planktonic growth due to a low trickling frequency. Only after some medium replacements to remove planktonic cells, higher gas consumption rates were recorded for the evolved culture. Interestingly, the evolved S. ovata had a relevant point mutation in the gene galU, encoding UDP-glucose pyrophosphorylase, an enzyme involved in the synthesis of extracellular polysaccharides. Overall, this study demonstrates that cell attachment by S. ovata was increased through adaptive laboratory evolution, offering the prospect of investigating the importance of biofilm formation in biofilm-based gas fermentation reactors. IMPORTANCEAcetogenic bacteria are attractive biocatalysts for the conversion of CO2 with H2 into acetate, as in gas fermentation and microbial electrosynthesis. Both biotechnologies could benefit from biofilm formation, since biofilm formation retains the catalytic activity inside continuously operated reactors. In addition, biofilm-based gas fermentation reactor systems are advantageous to improve the gas to liquid mass transfer of H2 and CO2. Moreover, microbial electrosynthesis benefits from biofilms on cathodes to consume H2 as soon as it gets generated. Acetogenic bacteria are however often found to only form thin or sparse biofilms. In the current study, we demonstrated that adaptive laboratory evolution is a useful strategy to increase the biofilm formation capabilities of the acetogen, Sporomusa ovata. The obtained biofilm improved S. ovata is of interest to deepen our fundamental understanding of biofilm formation by acetogens, as well as to assess the importance of biofilm formation for the performance of biofilm-based bioreactors.

microbiology↗

bioRxiv2025

Maize root growth, Oxygen and N availability drive formation of N2O hotspots in soil

Plant roots modify all major controls of denitrification in soils, particularly the availability of the main substrates (NO3- and Corg), soil moisture, soil O2 content, and root-associated microbial communities, and thus play an important role in N2O formation. Direct in-situ measurements of N2O concentrations in the rhizosphere are lacking, yet crucial to understanding how rhizosphere denitrification contributes to overall N2O emissions from soil. We equipped rhizoboxes with O2-sensitive planar optodes to simultaneously monitor root growth and rhizosphere/soil O2 concentrations. We measured soil surface N2O fluxes and linked them to root growth, soil moisture, and root/soil O2 concentrations. Based on root growth and O2 concentrations, we identified regions of interest (ROI) and sampled small soil volumes, which were analyzed for C, N, abundance of microbial denitrifiers (nirK, nirS) and N2O reducers (nosZI, nosZII), and soil N2O concentrations. Plant roots determined depth gradients of nutrients and denitrification gene abundances in the soil of the rhizoboxes with higher resource availability (NO3-, DOC) and lower soil moisture in the upper soil layers, which also had higher abundances of total bacteria, nirK and nosZII. We anticipate that these uppermost soil layers largely contributed to N2O formation. For the first time we were able to show high in-situ N2O concentrations with distinct depth profiles around roots, and O2 and N availability controlling N2O production at the process scale.

plant biology↗

bioRxiv2024

A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins.

Lipoproteins are essential for lipid transport in all bilaterians. A single Apolipoprotein B (ApoB) molecule is the inseparable structural scaffold of each ApoB-containing lipoprotein (B-lps), which are responsible for transporting lipids to peripheral tissues. The cellular mechanisms that regulate ApoB and B-lp production, secretion, transport, and degradation remain to be fully defined. In humans, elevated levels of vascular B-lps play a causative role in cardiovascular disease. Previously, we have detailed that human B-lp biology is remarkably conserved in the zebrafish using an in vivo chemiluminescent reporter of ApoB (LipoGlo) that does not disrupt ApoB function. Thus, the LipoGlo model is an ideal system for identifying novel mechanisms of ApoB modulation and, due to the ability of zebrafish to generate many progeny, is particularly amenable to large-scale phenotypic drug screening. Here, we report a screen of roughly 3000 compounds that identified 49 unique ApoB-lowering hits. Nineteen hits passed orthogonal screening criteria and seven were subjected to extensive phenotyping. A licorice root component, enoxolone, significantly lowered B-lps only in animals that express a functional allele of the nuclear hormone receptor Hepatocyte Nuclear Factor 4 (HNF4). Consistent with this result, inhibitors of HNF4 also reduce B-lp levels. These data demonstrate that mechanism(s) of action can be rapidly determined from a whole animal zebrafish phenotypic screen. Given the well documented role of HNF4 in human B-lp biology, these data validate the LipoGlo screening platform for identifying small molecule modulators of B-lps that play a critical role in a leading cause of worldwide mortality.

physiology↗

bioRxiv2024

Oxygen partitioning into biomolecular condensates is governed by excluded volume

Biomolecular condensates form through the self-assembly of proteins and nucleic acids to create dynamic compartments in cells. By concentrating specific molecules, condensates establish distinct microenvironments that regulate biochemical reactions in time and space. Macromolecules and metabolites partition into condensates depending on their interactions with the macromolecular constituents, however, the partitioning of gases has not been explored. We investigated oxygen partitioning into condensates formed by intrinsically disordered repeat proteins with systematic sequence variations using microelectrodes and phosphorescence lifetime imaging microscopy (PLIM). Unlike other hydrophobic metabolites, oxygen is partially excluded from the condensate with partitioning constants more strongly modulated by changes in protein length than hydrophobicity. For repeat proteins, the dense phase protein concentration drops with chain length resulting in a looser condensate. We found that oxygen partitioning is anti-correlated with dense phase protein concentration. Several mechanisms could explain such an anti-correlation including excluded volume or salting out effects. Molecular dynamics simulations suggest that oxygen does not form strong and specific interactions with the scaffold and is dynamic on the nanosecond timescale. Biomolecular condensates thus result in variation of oxygen concentrations on nanometer length-scales, which may tune the oxygen concentration available for biochemical reactions within the cell.

biophysics↗

bioRxiv2023

Variability in single-cell oxygen consumption kinetics

We combined microfabricated devices with multiparameter identification algorithms to probe the variability in size-dependent oxygen consumption parameters of single human hepatic cells. We demonstrate that single cells exhibit an oxygen-dependent metabolic rate, typical of Michaelis-Menten kinetics, and that their maximal oxygen consumption is significantly lower than that of monolayers or 3D hepatic cell aggregates. Notably, we found that clusters of two or more cells competing for a limited oxygen supply reduced their maximal single-cell consumption rate, highlighting their ability to adapt to local resource availability and the presence of nearby cells. Next, we used our high-throughput approach to characterize the covariance of size and oxygen consumption within a cell population. The results show that cooperative behaviour emerges in cell clusters, and that single-cell size and metabolism can be described by a lognormal joint probability density. Our study thus serves as a foundation to connect the metabolic activity of single human hepatocytes to their tissue-or organ-level metabolism as well as describe its size-related variability through scaling laws.

bioengineering↗

bioRxiv2019

Substantial near-infrared radiation-driven photosynthesis of chlorophyll f-containing cyanobacteria in a natural habitat

Far-red absorbing chlorophylls are constitutively present as Chl d in the cyanobacterium Acaryochloris marina, or dynamically expressed by synthesis of Chl f and red-shifted phycobilins via far-red light photoacclimation in a range of cyanobacteria, which enables them to use near-infrared-radiation (NIR) for oxygenic photosynthesis. While the biochemistry and molecular physiology of Chl f-containing cyanobacteria has been unraveled in culture studies, their ecological significance remains unexplored and no data on their in situ activity exist. With a novel combination of hyperspectral imaging, confocal laser scanning microscopy, and nanoparticle-based O2 imaging, we demonstrate substantial NIR-driven oxygenic photosynthesis by endolithic, Chl f-containing cyanobacteria within natural beachrock biofilms that are widespread on (sub)tropical coastlines. This indicates an important role of NIR-driven oxygenic photosynthesis in primary production of endolithic and other shaded habitats.\n\nImpact statementCyanobacteria with chlorophyll f show substantial near-infrared radiation-driven photosynthesis in intertidal habitats.

ecology↗

bioRxiv2018

In vitro community synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

Composition and development of naturally occurring microbial communities is defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause community synergies where the community is able to outperform it single species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here we show how pH stabilisation of the environment through the metabolic activity of specific community members acts as a positive inter-species interaction driving in vitro community synergy in a model consortium of four co-isolated soil bacteria: Microbacterium oxydans, Xanthomonas retroflexus, Stenotrophomonas rhizophila and Paenibacillus amylolyticus. Using micro-sensor pH measurements to show how individual species change the local pH micro-environment, and how co-cultivation leads to a stabilised pH regime over time. Specifically, in vitro acid production from Paenibacillus amylolyticus and alkali production primarily from Xanthomonas retroflexus lead to an overall pH stabilisation of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on media type and media concentration, however similar pH drift from the individual species could be observed across media variants.\n\nImportanceWe show that in vitro metabolic activity of individual members of a synthetic, co- isolated model community presenting community synergistic growth arises through the inter-species interaction of pH stabilization of the community micro-environment. The observed inter-species interaction is highly media specific and most pronounced under high nutrient availability. This adds to the growing diversity of identified community interactions leading to enhanced community growth.

microbiology↗